Description of Research

Supporting Information & Structures

Programs & Software

Useful Resources

James Group

Schedules



Main page



Contact information

Useful NMR Resources


Structure Databases
Display and Graphics
Nucleic Acids
Proteins
Meetings
Other NMR Research Groups
Commercial NMR Sites
Stable Isotopes


Structure Databases

Display and Graphics

  • PDB3D: Realtime 3D Molecule Renderer for the WWW running as interpreted Java

  • PDB to VRML converter

  • Proteins in VRML Virtual Reality Modeling language

  • Rasmol & Chime RasMol is free software for looking at molecular structures. Chime shows molecules inside a web page, freeware for Mac, PC and SGI

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Nucleic Acids

  • ICGEBnet DNA tools This server calculates various parameters from DNA sequences and plots them. Three programs: plot.it, bend.it, curve.it.

  • Curves Helical Analysis of Irregular Nucleic Acids, by R. Lavery and H. Sklenar

  • mfold Interactive server to predict RNA folding, by M. Zuker

  • RNA the journal of the RNA Society

  • Rnadraw RNA drawing and analysis tools, for MS Windows

  • RNA World the most comprehensive RNA site, at IMB Jena. Many links for programs, structural and sequence databases.

  • SCOP: Nucleic Acids Structural Classification of Proteins classifies nucleic acids too. Each entry can be viewed in VRML or RasMol.

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Proteins

  • Baylor College of Medicine Search Launcher Starting point for sequence and pattern searches, alignments and secondary structure predition

  • Biotech Validation Suite for Protein Structures just upload your coordinates to have your structure checked by PROCHECK, SurVol, and WhatIf

  • EMBL:the PredictProtein server generate multiple sequence alignments, secondary structure, residue solvent accessibility, transmembrane helices, topology for transmembrane proteins, and fold recognition.

  • ExPASy THE molecular biology server: Swiss Prot, Prosite, Enzyme, CD40Lbase, and Seqence Analysis bibliographic reference database

  • NOAMI NAOMI is a computer program system for studying, manipulating and predicting features and properties of three-dimensional protein structures. It runs only on Silicon Graphics SGI compuer systems. by S. Brocklehurst. Employs fuzzy logic to define elements of structure, and other novel algorithms.

  • Protein Motions Database Protein motions can be viewed in VRML or as a movie. Movies are either CPK, stick, or ribbon and in stereo. Great site.

  • Protein Society The journal Protein Science here, also kinemages and registration for the Protein Society meeting.

  • PROWL - Skirball Databases on peptides, nucleic acids and carbohydrates. Calculators for molecular weights. Tending towards use for mass spectroscopy. Also and entry point for many web resources.

  • Univ College London Biochemistry Biomolecular Structure Group Protein Structure Analysis, Sequence Analysis, Structure Classification (CATH)

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Links to NMR Resources

Meetings

NMR Research Groups

Commercial NMR Sites

Stable Isotopes